Welcome to the estim8 documentation!#
estim8 is a Python package for parameter estimation and uncertainty quantification in dynamical biological models. It is designed to be easy to use, and to provide a consistent interface for a variety of parameter estimation and uncertainty quantification methods.
The framework features model definition using a broad range of third-party modeling tools comliant to the FMI standard, such as the open sourc environment OpenModelica.
It implements special features for common biotechnological applications, like e.g. fitting multiple experimental replicates. Model optimization utilizes a variety of metaheuristic optimization algorithms, including the generalized islands approach from pygmo as well as functions from scipy.optimize.
Installation#
It is highly recommended to use a conda or preferably a mamba environment manager.
Installation from PyPi#
It is advised to create a fresh virtual environent using mamba (or conda alternatively) with any Python>=3.10,<3.14:
mamba create --name estim8 python=3.13
mamba activate estim8
Note
Not all dependencies are packaged with the PyPI version. In order to use pygmo optimizers, the package needs to be installed manually. When using federated setups on Windows, additionally install m2w64-toolchain.
These packages need to be installed before installing estim8!
mamba install -c conda-forge pygmo m2w64-toolchain
estim8 can then easily be installed using pip:
pip install estim8
Development installation#
Download the source code repository to your computer, best by using git:
Navigate to the directory of your computer where you want the repository to be located and open a terminal.
Clone the source code repository via
git clone https://github.com/JuBiotech/estim8.gitChange into the dowloaded directory
cd estim8
It is advised to create a fresh virtual environent:
mamba create --name estim8 python==3.10
mamba activate estim8
mamba env update --name estim8 --file environment.yml
Tutorials